| regen_blast_4 |
| ID: | 1673004360 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 482 (473) | ||
| Sequences: | 23353 (15606) | ||
| Seq/Len: | 49.372 | ||
| Nf(neff/√len): | 717.6 |
HHblits Results: (2016_02)
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 329_A | 392_L | 5.001 | 1.00 |
| 382_N | 385_E | 4.018 | 1.00 |
| 291_E | 338_H | 3.795 | 1.00 |
| 382_N | 387_N | 3.724 | 1.00 |
| 304_D | 308_E | 3.681 | 1.00 |
| 300_K | 304_D | 3.590 | 1.00 |
| 288_A | 434_L | 3.463 | 1.00 |
| 298_V | 326_Y | 3.419 | 1.00 |
| 301_R | 389_D | 3.381 | 1.00 |
| 352_S | 362_E | 3.273 | 1.00 |
| 226_M | 263_M | 3.229 | 1.00 |
| 375_R | 384_S | 3.032 | 1.00 |
| 328_E | 431_M | 2.966 | 1.00 |
| 288_A | 334_T | 2.952 | 1.00 |
| 302_V | 330_V | 2.937 | 1.00 |
| 144_T | 433_I | 2.894 | 1.00 |
| 284_M | 430_M | 2.890 | 1.00 |
| 361_P | 364_A | 2.737 | 1.00 |
| 141_S | 289_M | 2.655 | 1.00 |
| 25_T | 29_H | 2.651 | 1.00 |
| 303_Q | 442_D | 2.636 | 1.00 |
| 302_V | 438_M | 2.623 | 1.00 |
| 300_K | 442_D | 2.571 | 1.00 |
| 302_V | 327_L | 2.566 | 1.00 |
| 219_E | 223_K | 2.535 | 1.00 |
| 301_R | 326_Y | 2.529 | 1.00 |
| 288_A | 330_V | 2.529 | 1.00 |
| 354_T | 359_T | 2.513 | 1.00 |
| 34_I | 47_V | 2.495 | 1.00 |
| 377_P | 383_P | 2.391 | 1.00 |
| 352_S | 359_T | 2.387 | 1.00 |
| 225_R | 244_D | 2.364 | 1.00 |
| 223_K | 227_N | 2.284 | 1.00 |
| 303_Q | 307_E | 2.261 | 1.00 |
| 141_S | 285_V | 2.223 | 1.00 |
| 331_C | 430_M | 2.222 | 1.00 |
| 299_M | 442_D | 2.168 | 1.00 |
| 223_K | 263_M | 2.140 | 1.00 |
| 121_R | 436_S | 2.119 | 1.00 |
| 437_L | 443_W | 2.104 | 1.00 |
| 337_L | 375_R | 2.081 | 1.00 |
| 288_A | 292_I | 2.072 | 1.00 |
| 12_S | 15_F | 2.069 | 1.00 |
| 118_H | 151_N | 2.068 | 1.00 |
| 299_M | 303_Q | 2.068 | 1.00 |
| 300_K | 303_Q | 2.054 | 1.00 |
| 63_S | 351_K | 2.044 | 1.00 |
| 371_W | 375_R | 1.997 | 1.00 |
| 285_V | 433_I | 1.993 | 1.00 |
| 291_E | 295_D | 1.987 | 1.00 |
| 220_P | 224_E | 1.966 | 1.00 |
| 377_P | 384_S | 1.948 | 1.00 |
| 330_V | 386_F | 1.943 | 1.00 |
| 47_V | 56_I | 1.922 | 1.00 |
| 23_E | 26_K | 1.914 | 1.00 |
| 219_E | 267_K | 1.895 | 1.00 |
| 128_Y | 440_S | 1.885 | 1.00 |
| 295_D | 298_V | 1.882 | 1.00 |
| 212_K | 216_K | 1.876 | 1.00 |
| 354_T | 357_G | 1.863 | 1.00 |
| 8_P | 11_G | 1.860 | 1.00 |
| 53_A | 373_I | 1.826 | 1.00 |
| 10_V | 14_P | 1.814 | 1.00 |
| 26_K | 29_H | 1.812 | 1.00 |
| 26_K | 30_Q | 1.807 | 1.00 |
| 349_P | 360_V | 1.797 | 1.00 |
| 216_K | 220_P | 1.791 | 1.00 |
| 7_L | 10_V | 1.776 | 1.00 |
| 289_M | 437_L | 1.776 | 1.00 |
| 306_L | 435_A | 1.775 | 1.00 |
| 227_N | 231_T | 1.774 | 1.00 |
| 326_Y | 389_D | 1.774 | 1.00 |
| 293_F | 299_M | 1.761 | 1.00 |
| 298_V | 330_V | 1.756 | 1.00 |
| 219_E | 263_M | 1.751 | 1.00 |
| 25_T | 372_A | 1.740 | 1.00 |
| 317_E | 320_H | 1.722 | 1.00 |
| 307_E | 439_H | 1.699 | 1.00 |
| 419_R | 423_I | 1.693 | 1.00 |
| 120_V | 144_T | 1.684 | 1.00 |
| 309_I | 324_L | 1.680 | 1.00 |
| 292_I | 298_V | 1.668 | 1.00 |
| 64_F | 353_C | 1.659 | 1.00 |
| 305_E | 324_L | 1.656 | 1.00 |
| 291_E | 337_L | 1.616 | 1.00 |
| 36_K | 43_L | 1.611 | 1.00 |
| 314_N | 320_H | 1.599 | 1.00 |
| 328_E | 332_K | 1.593 | 1.00 |
| 262_T | 265_Q | 1.592 | 1.00 |
| 291_E | 334_T | 1.588 | 1.00 |
| 52_L | 356_G | 1.585 | 1.00 |
| 284_M | 340_P | 1.582 | 1.00 |
| 292_I | 299_M | 1.568 | 1.00 |
| 351_K | 362_E | 1.562 | 1.00 |
| 329_A | 389_D | 1.555 | 1.00 |
| 348_A | 363_G | 1.554 | 1.00 |
| 35_F | 46_V | 1.553 | 1.00 |
| 38_Y | 43_L | 1.550 | 1.00 |
| 174_K | 178_R | 1.543 | 1.00 |
| 3_G | 31_Y | 1.520 | 1.00 |
| 387_N | 393_N | 1.510 | 1.00 |
| 332_K | 410_F | 1.508 | 1.00 |
| 330_V | 334_T | 1.498 | 1.00 |
| 224_E | 228_S | 1.496 | 1.00 |
| 149_F | 277_G | 1.492 | 1.00 |
| 95_L | 269_L | 1.490 | 1.00 |
| 426_G | 430_M | 1.477 | 1.00 |
| 285_V | 430_M | 1.472 | 1.00 |
| 33_P | 49_S | 1.470 | 1.00 |
| 136_D | 139_E | 1.469 | 1.00 |
| 374_Q | 412_P | 1.457 | 1.00 |
| 3_G | 12_S | 1.451 | 1.00 |
| 292_I | 302_V | 1.439 | 1.00 |
| 117_R | 436_S | 1.434 | 1.00 |
| 306_L | 324_L | 1.434 | 1.00 |
| 303_Q | 438_M | 1.434 | 1.00 |
| 306_L | 327_L | 1.416 | 1.00 |
| 150_T | 158_F | 1.408 | 1.00 |
| 152_I | 425_L | 1.402 | 0.99 |
| 90_A | 94_N | 1.400 | 0.99 |
| 333_E | 336_R | 1.399 | 0.99 |
| 223_K | 226_M | 1.394 | 0.99 |
| 146_L | 278_T | 1.394 | 0.99 |
| 128_Y | 441_F | 1.393 | 0.99 |
| 215_D | 264_T | 1.388 | 0.99 |
| 224_E | 227_N | 1.387 | 0.99 |
| 144_T | 148_V | 1.385 | 0.99 |
| 45_I | 364_A | 1.380 | 0.99 |
| 352_S | 361_P | 1.376 | 0.99 |
| 290_T | 294_R | 1.372 | 0.99 |
| 29_H | 377_P | 1.372 | 0.99 |
| 247_Q | 251_E | 1.369 | 0.99 |
| 7_L | 14_P | 1.369 | 0.99 |
| 377_P | 381_E | 1.368 | 0.99 |
| 54_K | 58_A | 1.364 | 0.99 |
| 47_V | 52_L | 1.357 | 0.99 |
| 49_S | 52_L | 1.344 | 0.99 |
| 149_F | 153_I | 1.344 | 0.99 |
| 301_R | 304_D | 1.333 | 0.99 |
| 436_S | 440_S | 1.320 | 0.99 |
| 119_E | 151_N | 1.317 | 0.99 |
| 227_N | 230_S | 1.306 | 0.99 |
| 334_T | 386_F | 1.304 | 0.99 |
| 293_F | 443_W | 1.294 | 0.99 |
| 332_K | 427_E | 1.293 | 0.99 |
| 374_Q | 410_F | 1.292 | 0.99 |
| 381_E | 387_N | 1.290 | 0.99 |
| 215_D | 267_K | 1.290 | 0.99 |
| 221_T | 224_E | 1.288 | 0.99 |
| 310_V | 439_H | 1.282 | 0.99 |
| 335_F | 412_P | 1.269 | 0.99 |
| 444_K | 472_T | 1.268 | 0.99 |
| 53_A | 368_V | 1.266 | 0.99 |
| 156_K | 224_E | 1.264 | 0.99 |
| 288_A | 331_C | 1.258 | 0.99 |
| 23_E | 27_I | 1.252 | 0.99 |
| 171_N | 213_Q | 1.251 | 0.99 |
| 109_L | 428_K | 1.249 | 0.99 |
| 291_E | 294_R | 1.246 | 0.98 |
| 51_E | 54_K | 1.229 | 0.98 |
| 289_M | 434_L | 1.228 | 0.98 |
| 427_E | 431_M | 1.216 | 0.98 |
| 125_K | 128_Y | 1.206 | 0.98 |
| 425_L | 429_M | 1.203 | 0.98 |
| 209_D | 213_Q | 1.200 | 0.98 |
| 297_K | 301_R | 1.195 | 0.98 |
| 219_E | 264_T | 1.192 | 0.98 |
| 145_V | 281_T | 1.192 | 0.98 |
| 119_E | 122_K | 1.182 | 0.98 |
| 33_P | 378_R | 1.180 | 0.98 |
| 45_I | 360_V | 1.179 | 0.98 |
| 298_V | 389_D | 1.179 | 0.98 |
| 121_R | 125_K | 1.175 | 0.98 |
| 335_F | 410_F | 1.174 | 0.98 |
| 90_A | 93_R | 1.173 | 0.98 |
| 113_H | 117_R | 1.167 | 0.97 |
| 94_N | 265_Q | 1.165 | 0.97 |
| 117_R | 121_R | 1.160 | 0.97 |
| 325_K | 329_A | 1.154 | 0.97 |
| 298_V | 387_N | 1.153 | 0.97 |
| 302_V | 326_Y | 1.151 | 0.97 |
| 436_S | 439_H | 1.150 | 0.97 |
| 91_N | 94_N | 1.149 | 0.97 |
| 151_N | 157_G | 1.147 | 0.97 |
| 91_N | 265_Q | 1.147 | 0.97 |
| 416_G | 420_C | 1.143 | 0.97 |
| 138_N | 286_E | 1.142 | 0.97 |
| 304_D | 307_E | 1.127 | 0.97 |
| 34_I | 358_Y | 1.124 | 0.97 |
| 137_I | 289_M | 1.124 | 0.97 |
| 288_A | 386_F | 1.121 | 0.97 |
| 19_N | 22_Q | 1.118 | 0.96 |
| 126_Y | 140_I | 1.117 | 0.96 |
| 6_G | 12_S | 1.116 | 0.96 |
| 124_V | 441_F | 1.109 | 0.96 |
| 208_K | 212_K | 1.101 | 0.96 |
| 413_F | 416_G | 1.099 | 0.96 |
| 47_V | 53_A | 1.094 | 0.96 |
| 51_E | 356_G | 1.089 | 0.96 |
| 369_N | 372_A | 1.082 | 0.96 |
| 27_I | 35_F | 1.077 | 0.95 |
| 124_V | 436_S | 1.066 | 0.95 |
| 65_A | 350_I | 1.066 | 0.95 |
| 327_L | 330_V | 1.063 | 0.95 |
| 119_E | 157_G | 1.062 | 0.95 |
| 244_D | 247_Q | 1.062 | 0.95 |
| 48_N | 376_D | 1.062 | 0.95 |
| 298_V | 301_R | 1.060 | 0.95 |
| 289_M | 438_M | 1.059 | 0.95 |
| 370_V | 411_L | 1.058 | 0.95 |
| 229_R | 251_E | 1.058 | 0.95 |
| 284_M | 334_T | 1.048 | 0.94 |
| 326_Y | 388_P | 1.048 | 0.94 |
| 51_E | 378_R | 1.048 | 0.94 |
| 220_P | 223_K | 1.043 | 0.94 |
| 122_K | 125_K | 1.043 | 0.94 |
| 297_K | 300_K | 1.042 | 0.94 |
| 321_I | 431_M | 1.042 | 0.94 |
| 139_E | 143_S | 1.042 | 0.94 |
| 348_A | 365_T | 1.039 | 0.94 |
| 215_D | 219_E | 1.036 | 0.94 |
| 243_K | 251_E | 1.035 | 0.94 |
| 241_G | 251_E | 1.030 | 0.94 |
| 306_L | 439_H | 1.026 | 0.94 |
| 444_K | 470_V | 1.022 | 0.93 |
| 331_C | 431_M | 1.021 | 0.93 |
| 377_P | 382_N | 1.013 | 0.93 |
| 141_S | 286_E | 1.012 | 0.93 |
| 309_I | 323_K | 1.010 | 0.93 |
| 293_F | 469_A | 1.008 | 0.93 |
| 34_I | 52_L | 1.007 | 0.93 |
| 384_S | 387_N | 1.004 | 0.93 |
| 360_V | 366_I | 1.004 | 0.93 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 4r21A | 2 | 0.8734 | 100 | 0.102 | Contact Map |
| 3pm0A | 1 | 0.9274 | 100 | 0.108 | Contact Map |
| 3czhA | 2 | 0.9461 | 100 | 0.115 | Contact Map |
| 3tbgA | 4 | 0.9398 | 100 | 0.116 | Contact Map |
| 2hi4A | 1 | 0.9481 | 100 | 0.116 | Contact Map |
| 3swzA | 4 | 0.9544 | 100 | 0.131 | Contact Map |
| 3k9vA | 2 | 0.9212 | 100 | 0.133 | Contact Map |
| 1r9oA | 1 | 0.9129 | 100 | 0.136 | Contact Map |
| 3nxuA | 2 | 0.9149 | 100 | 0.138 | Contact Map |
| 2fdvA | 4 | 0.9378 | 100 | 0.141 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)